• Posts 4
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  • Name Juan Gutierrez
  • Birthday April 07,1962 (55 years)
  • Location: New Jersey
  • Occupation: Physician
  • Hobbies: Science
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Impossible to have access to my Brains
It's been many hours without any action or statement. Really not acceptable.
I was at work with no access to my references because I couldn't sync to my laptop.
Generating a Citation Forest
Liz Ann,

I have been using TB for reference management for quite some time, and I have experimented with different ways to do it. I'm using TB9 now, because the preview of files (mostly pdfs in my case) really changed my approach. The advantage of TB is that you can organize the information in many different ways, resting assured that no matter how you do it, you can always retrieve it almost instantly with the search function. I organize my references in TB not because I want to have a way of retrieving something fast, because 99% of the time I can do that just using the search function with very few strokes (even just using the search function of the Mac OS), but because I want to explore and see how the information relates to each other and to how many hierarchies it belongs. That is something that most specialized reference managers can't do well, or at least they can't do visually. If it helps, this is a bird's eye view of how I organize my references:
- They are organized mostly by topics. Topics are thoughts of the type "Topics" (very imaginative). In other systems topics would be keywords or tags, but using "thoughts" allows me to generate a visual structure or hierarchy of topics. For example, if I have an article on fluid resuscitation in sepsis, it resides under "Work-References" -> "Sepsis" -> "fluid resuscitation" (of course, the beauty is that it can also have other parent thoughts if it relates to more than one topic)
- The source (a medical or scientific journal in most cases) is the abbreviated name of the journal as a tag. In that way, when I look at the list of the references under fluid resuscitation, I can see that this particular reference was published in the "CritCareMed" (Critical Care Medicine) journal
- The name of the thought for the reference always include and starts with the year of publication, and is the original name of the article. In medicine and science, sometimes that makes for very long thought names. I experimented with assigned shorter names in the past, but that can lead to duplications when you are dealing with thousands of references like in my case (my TB is going over 10K thoughts now). I include the year first, because if a see that a review on septic shock is 10 years old, I know that the article is not up-to-date and might be stale.
- I use link types. If an article relates to another but it's not worth to create a separate topic, I just link them. But if it's an editorial on that article, I use a special link of different color and with the label "Editorial" (again, very imaginative). If the article is a review on a published book, the link will be of a different color with the label "Review"
- I use plain thought  types for the articles in journals, but books will be a different thought type (three types actually, one for books that I have read, one for books that I own but haven't read, and one for books that I don't own but I might consider to buy).
- I use a few additional tags for special things. I have a red-colored tag for "Key-Reference", I have one for my own publications, one for "graphic" or "photo"
- I don't store in the TB the author information, except for selected authors, and when I do I will have a thought for the author, with the child thought as his/her publications.
Again , the whole idea is that when I see a reference, I can immediately see from the list of references under what topics is under, what's the year of publication, what journal, and if it's linked to other references, and if it's an important reference or not. Of course, the ability to preview the pdf in TB9 adds even more (visual) information.
Hope this helps.
Import Imperfection (#3640)
I wonder if something related is happening with my brain. Since yesterday, when I added a large number of files, the sync is failing consistently. It goes all the way to "report 100% complete", but then goes into "sync failed: unknown error". Some of the files I added had very long filenames (I work in a Mac, a system that usually doesn't care about that). I have been trying to manually hunt those long filenames and shortened them, but the problem persists. Does anybody know of a way to hunt for those files other than manually?
(For context my brain has 7,521 thoughts with 3,000 internal attachments, internal file size of 5.11 GB; working on an iMac retina 5K 3.2 GHz Intel Core i% with 16 GB memory, on Sierra 10.12.3).
The Brain as a reference manager

I wonder if others have been using the Brain for professional references.
I have a few thousand reference papers on the brain in the form of pdfs, some work-related (pediatric critical care medicine) and some part of my personal interests. I have them organized by topics, taking advantage of the ability to have one reference under multiple topics, and also cross-linking related papers as sister thoughts. The title of the thought is usually the year the paper was published, followed by the main idea or the main piece of information I gathered from the paper, and the journal in parenthesis (e.g. "2015- Medication X does not work in ARDS (JAMA)"). I use quick view to quickly glance at the paper if I need more info, but for many of these thoughts I use the "capture icon" tool to assign the quick view screenshot as the icon for that thought. (I guess that won't be necessary in Brain 9, as it gives you a preview of the pdf in the thought pane). I use keywords sparingly (e.g. "key" for a very important paper).
I tried many other programs to organize my references, including dedicated reference managers as well as other programs such as EverNote and DevonThink, but none could match the flexibility of the Brain, its visual representation of where a paper belongs and what it's related to, and the ability to cross link disparate pieces of information. If a paper required a lot of hand written notes or a paper mind map, I scan that note and then link it to the paper, so that I have my own notes and thoughts on the paper right on the brain.
Again, I'm curious if there are others using the Brain this way.

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